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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGGAAGAGCTTCACCTACAGCAGTAGTATCAACATTGCCGTGGCAGTGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacactttaccatgcacaatgagtgttgatatttttgatgattttttttaaataaatggttacttgctggtttatgcag

Basic information

species Zea mays
transcript GRMZM2G165176_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165176_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g08170.1 (Oryza sativa), 5'ss of exon 2
GGATGGGAAGAGCTTCACCTACAGCAGTAGTATCAACATTGCCGTGGCAGTGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacactt-----taccatgcacaatgagtgttgatatttttgatgattttttttaa-ataaatggttacttgctggtttatgcag
||||||||||||||||| |||| ||| || || ||||| || |||||||||||||| ||||||||||||||||| ||||| |||| |||||||||||||| | ||| | | | | | ||| | ||| ||||| | | || | ||||||||| ||| ||||||||||||
AGATGGGAAGAGCTTCACTTACAACAGCAGCATAAACATCGCTGTGGCAGTGGCCATCGATGGTGGGTTGATTACGCCAGTGCTTCCTGATGCTGATAAGgtacagtgcttgtaattgttgcatatacttaaaattggtgtttatgatggcgtctcttgatgaaaatggttaattgttggtttatgcag

upper sequence: GRMZM2G165176_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA20G31630.1 (Glycine max), 5'ss of exon 3
GGATGGGAAGAGCTTCACCTACAGCAGTAGTATCAACATTGCCGTGGCAGTGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgt---caaacactttaccatgcacaatgagtgttgatatttttgatgattttttttaaataa-atggttacttgctggtttatgcag-------------------
||||| || ||||| || || | || || ||||| ||||| || || ||||| ||||||||||| ||||||||||||| ||||| | |||||||||||| | || ||| || | || | | | | |||| | | |||| |||||| || || |||
AGATGGTAATAGCTTTACATATAATAGCAGCATCAATATTGCAGTTGCTGTGGCTATAGATGGTGGACTGATTACACCAGTGCTTCAGGGTGCTGATAAGgttttccaatactctagtttaagcagcttctagtccccccatctcccacttttctaatataagatggttctttattgtaaaatggtatatttgatgtatattgtag

upper sequence: GRMZM2G165176_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA10G35960.2 (Glycine max), 5'ss of exon 3
GGATGGGAAGAGCTTCACCTACAGCAGTAGTATCAACATTGCCGTGGCAGTGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacactttaccatgcacaatgagtgttgatatttttgatg---attttttttaaataa-atggttacttgctggtttatgcag-----------------------
||||| || ||||| || || | || || ||||| ||||| || || ||||| |||||||| || |||||||||||||| ||||| | |||||||||||| | || | | | | | | || | |||| | | |||| |||||| || || |||
AGATGGTAATAGCTTTACATATAATAGCAGCATCAATATTGCTGTTGCTGTGGCTATAGATGGCGGATTGATTACACCAGTGCTTCAGGGTGCTGATAAGgtttaccaatactctaatttaagcagcttctaatctccccacctcctgcttttctaatataagatggttctttattgtaaaatggtatatttatttgatgtatattgtag

upper sequence: GRMZM2G165176_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv18s0072g01000.t01 (Vitis vinifera), 5'ss of exon 2
GGATGGGAAGAGCTTCACCTACAGCAGTAGTATCAACATTGCCGTGGCAGTGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacactttac-catgcacaa-tgagtgttgatatttttgatgattttttttaaataaatggttacttgctggtttatgcag
||||| |||||||| || || | |||||||||||| ||||| || ||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| | | | | ||| || | | | ||| | ||| |||| | | || ||| |||| || | ||
AGATGGTAAGAGCTTTACATATAACAGTAGTATCAATATTGCGGTTGCAGTGGCCATAGATGGTGGGTTGATTACACCAGTGCTTCAGGATGCTGATAAGgtttgttaatctgttcttgctaaacttaattttggc-taccctatggcttttcaagagttaa--attaattgcaatttattatag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71422995|gb|DR805914.1|DR805914
EST:     TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
EST: gi|31349635|gb|CD433992.1|CD433992
EST:     TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
EST: gi|50333015|gb|CO528141.1|CO528141
EST:     TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
EST: gi|148963616|gb|EE014658.2|EE014658
EST:     GGCCATAGATGGTGGGTGGATTACACCAGTTCTTCAAGATGGTGATAAGG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGC
genomic: GGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAA-Ggtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGC
EST: gi|149089772|gb|EE179047.2|EE179047
EST:     TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
EST: gi|101400418|gb|EB822024.1|EB822024
EST:     TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
EST: gi|71430961|gb|DR812011.1|DR812011
EST:     TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
EST: gi|37398364|gb|CF636494.1|CF636494
EST:     TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
EST: gi|31356951|gb|CD441308.1|CD441308
EST:     TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
EST: gi|211076029|gb|FL472760.1|FL472760
EST:     TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAG                         CTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG
genomic: TGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 98

GGATGGGAAGAGCTTCACCTACAGCAGTAGTATCAACATTGCCGTGGCAGTGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCGCGAGCAAAGCAGTTGCAGCCCCATGAGTACAACTCTG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 70

GGATGGGAAGAGCTTCACCTACAGCAGTAGTATCAACATTGCCGTGGCAGTGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCGCGAGCAAAGCAGTTGCAGCCCCATGAGTACAACTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 25

GGATGGGAAGAGCTTCACCTACAGCAGTAGTATCAACATTGCCGTGGCAGTGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCGCGAGCAAAGCAGTTGCAGCCCCATGAGTACAACTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 233

GGATGGGAAGAGCTTCACCTACAGCAGTAGTATCAACATTGCCGTGGCAGTGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacact ... gtttatgcagCTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCGCGAGCAAAGCAGTTGCAGCCCCATGAGTACAACTCTG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGGAAGAGCTTCACCTACAGCAGTAGTATCAACATTGCCGTGGCAGTGGCCATAGATGGTGGGTTGATTACACCAGTTCTTCAAGATGCTGATAAGgtcaaacactttaccatgcacaatgagtgttgatatttttgatgattttttttaaataaatggttacttgctggtttatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT